Perelman School of Medicine at the University of Pennsylvania

Liquid Biopsy Core

Publications

Impact of Interobserver Variability in Manual Segmentation of Non-Small Cell Lung Cancer (NSCLC) Applying Low-Rank Radiomic Representation on Computed Tomography.
Hershman M, Yousefi B, Serletti L, Galperin-Aizenberg M, Roshkovan L, Luna JM, Thompson JC, Aggarwal C, Carpenter EL, Kontos D, Katz SI. Cancers. 2021 Nov 28;13(23)

Racial Disparities in 30-Day Outcomes Following Index Admission for COVID-19.
Nimgaonkar V, Thompson JC, Pantalone L, Cook T, Kontos D, McCarthy AM, Carpenter EL. Frontiers in medicine. 2021;8:750650 Epub 2021 Nov 2

EUS-based Pancreatic Cancer Surveillance in BRCA1/BRCA2/PALB2/ATM Carriers Without a Family History of Pancreatic Cancer.
Katona BW, Long JM, Ahmad NA, Attalla S, Bradbury AR, Carpenter EL, Clark DF, Constantino G, Das KK, Domchek SM, Dudzik C, Ebrahimzadeh J, Ginsberg GG, Heiman J, Kochman ML, Maxwell KN, McKenna DB, Powers J, Shah PD, Wangensteen KJ, Rustgi AK. Cancer prevention research (Philadelphia, Pa.). 2021 Nov;14(11):1033-1040 Epub 2021 Aug 2

Optimization of Sources of Circulating Cell-Free DNA Variability for Downstream Molecular Analysis.
Till JE, Black TA, Gentile C, Abdalla A, Wang Z, Sangha HK, Roth JJ, Sussman R, Yee SS, O'Hara MH, Thompson JC, Aggarwal C, Hwang WT, Elenitoba-Johnson KSJ, Carpenter EL. The Journal of molecular diagnostics : JMD. 2021 Nov;23(11):1545-1552 Epub 2021 Aug 25

THSB2 as a prognostic biomarker for patients diagnosed with metastatic pancreatic ductal adenocarcinoma.
Gimotty PA, Till JE, Udgata S, Takenaka N, Yee SS, LaRiviere MJ, O'Hara MH, Reiss KA, O'Dwyer P, Katona BW, Herman D, Carpenter EL, Zaret KS. Oncotarget. 2021 Oct 26;12(22):2266-2272

Plasma Cell-Free DNA Genotyping: From an Emerging Concept to a Standard-of-Care Tool in Metastatic Non-Small Cell Lung Cancer.
Gray J, Thompson JC, Carpenter EL, Elkhouly E, Aggarwal C. The oncologist. 2021 Oct;26(10):e1812-e1821 Epub 2021 Jul 26

MYC levels regulate metastatic heterogeneity in pancreatic adenocarcinoma.
Maddipati R, Norgard RJ, Baslan T, Rathi KS, Zhang A, Saeid A, Higashihara T, Wu F, Kumar A, Annamalai V, Bhattacharya S, Raman P, Adkisson CA, Pitarresi JR, Wengyn MD, Yamazoe T, Li J, Balli D, LaRiviere MJ, Ngo TC, Folkert IW, Millstein ID, Bermeo J, Carpenter EL, McAuliffe JC, Oktay MH, Brekken RA, Lowe SW, Iacobuzio-Donahue CA, Notta F, Stanger BZ. Cancer discovery. 2021 Sep 22

Blood-based gene expression signature associated with metastatic castrate-resistant prostate cancer patient response to abiraterone plus prednisone or enzalutamide.
Haas NB, LaRiviere MJ, Buckingham TH, Cherkas Y, Calara-Nielsen K, Foulk B, Patel J, Gross S, Smirnov D, Vaughn DJ, Amaravadi R, Wellen KE, Savitch SL, Majmundar KJ, Black TA, Yee SS, He M, Min EJ, Long Q, Jones JO, Pal SK, Carpenter EL. Prostate cancer and prostatic diseases. 2021 Jun;24(2):448-456 Epub 2020 Oct 2

Combining radiomic phenotypes of non-small cell lung cancer with liquid biopsy data may improve prediction of response to EGFR inhibitors.
Yousefi B, LaRiviere MJ, Cohen EA, Buckingham TH, Yee SS, Black TA, Chien AL, Noël P, Hwang WT, Katz SI, Aggarwal C, Thompson JC, Carpenter EL, Kontos D. Scientific reports. 2021 May 11;11(1):9984

Serial Monitoring of Circulating Tumor DNA by Next-Generation Gene Sequencing as a Biomarker of Response and Survival in Patients With Advanced NSCLC Receiving Pembrolizumab-Based Therapy.
Thompson JC, Carpenter EL, Silva BA, Rosenstein J, Chien AL, Quinn K, Espenschied CR, Mak A, Kiedrowski LA, Lefterova M, Nagy RJ, Katz SI, Yee SS, Black TA, Singh AP, Ciunci CA, Bauml JM, Cohen RB, Langer CJ, Aggarwal C. JCO precision oncology. 2021;5 Epub 2021 Mar 19

Systemic inflammation is a determinant of outcomes of CD40 agonist-based therapy in pancreatic cancer patients.
Wattenberg MM, Herrera VM, Giannone MA, Gladney WL, Carpenter EL, Beatty GL. JCI insight. 2021 Mar 8;6(5)

Plasma Tumor Mutation Burden and Response to Pembrolizumab-Response.
Aggarwal C, Thompson JC, Carpenter EL. Clinical cancer research : an official journal of the American Association for Cancer Research. 2021 Mar 1;27(5):1581

THBS2/CA19-9 Detecting Pancreatic Ductal Adenocarcinoma at Diagnosis Underperforms in Prediagnostic Detection: Implications for Biomarker Advancement.
Udgata S, Takenaka N, Bamlet WR, Oberg AL, Yee SS, Carpenter EL, Herman D, Kim J, Petersen GM, Zaret KS. Cancer prevention research (Philadelphia, Pa.). 2021 Feb;14(2):223-232 Epub 2020 Oct 16

A Pilot Study of Galunisertib plus Stereotactic Body Radiotherapy in Patients with Advanced Hepatocellular Carcinoma.
Reiss KA, Wattenberg MM, Damjanov N, Prechtel Dunphy E, Jacobs-Small M, Lubas MJ, Robinson J, Dicicco L, Garcia-Marcano L, Giannone MA, Karasic TB, Furth EE, Carpenter EL, Wojcieszynski AP, Vonderheide RH, Beatty GL, Ben-Josef E. Molecular cancer therapeutics. 2021 Feb;20(2):389-397 Epub 2020 Dec 2

Association of plasma cell-free DNA with survival in patients with IDH wild-type glioblastoma.
Bagley SJ, Till J, Abdalla A, Sangha HK, Yee SS, Freedman J, Black TA, Hussain J, Binder ZA, Brem S, Desai AS, O'Rourke DM, Long Q, Nabavizadeh SA, Carpenter EL. Neuro-oncology advances. 2021 Jan-Dec;3(1):vdab011 Epub 2021 Jan 16

CD40 agonistic monoclonal antibody APX005M (sotigalimab) and chemotherapy, with or without nivolumab, for the treatment of metastatic pancreatic adenocarcinoma: an open-label, multicentre, phase 1b study.
O'Hara MH, O'Reilly EM, Varadhachary G, Wolff RA, Wainberg ZA, Ko AH, Fisher G, Rahma O, Lyman JP, Cabanski CR, Mick R, Gherardini PF, Kitch LJ, Xu J, Samuel T, Karakunnel J, Fairchild J, Bucktrout S, LaVallee TM, Selinsky C, Till JE, Carpenter EL, Alanio C, Byrne KT, Chen RO, Trifan OC, Dugan U, Horak C, Hubbard-Lucey VM, Wherry EJ, Ibrahim R, Vonderheide RH. The Lancet. Oncology. 2021 Jan;22(1):118-131

Type 1 conventional dendritic cells are systemically dysregulated early in pancreatic carcinogenesis.
Lin JH, Huffman AP, Wattenberg MM, Walter DM, Carpenter EL, Feldser DM, Beatty GL, Furth EE, Vonderheide RH. The Journal of experimental medicine. 2020 Aug 3;217(8)

Plasma Tumor Mutation Burden and Response to Pembrolizumab-Response.
Aggarwal C, Thompson JC, Carpenter EL. Clinical cancer research : an official journal of the American Association for Cancer Research. 2020 Jul 1;26(13):3492

A Multianalyte Panel Consisting of Extracellular Vesicle miRNAs and mRNAs, cfDNA, and CA19-9 Shows Utility for Diagnosis and Staging of Pancreatic Ductal Adenocarcinoma.
Yang Z, LaRiviere MJ, Ko J, Till JE, Christensen T, Yee SS, Black TA, Tien K, Lin A, Shen H, Bhagwat N, Herman D, Adallah A, O'Hara MH, Vollmer CM, Katona BW, Stanger BZ, Issadore D, Carpenter EL. Clinical cancer research : an official journal of the American Association for Cancer Research. 2020 Jul 1;26(13):3248-3258 Epub 2020 Apr 16

Baseline Plasma Tumor Mutation Burden Predicts Response to Pembrolizumab-based Therapy in Patients with Metastatic Non-Small Cell Lung Cancer.
Aggarwal C, Thompson JC, Chien AL, Quinn KJ, Hwang WT, Black TA, Yee SS, Christensen TE, LaRiviere MJ, Silva BA, Banks KC, Nagy RJ, Helman E, Berman AT, Ciunci CA, Singh AP, Wasser JS, Bauml JM, Langer CJ, Cohen RB, Carpenter EL. Clinical cancer research : an official journal of the American Association for Cancer Research. 2020 May 15;26(10):2354-2361 Epub 2020 Feb 26

Plasma cfDNA in Glioblastoma-Response.
Bagley SJ, Carpenter EL. Clinical cancer research : an official journal of the American Association for Cancer Research. 2020 May 1;26(9):2276

Highly specific enrichment of rare nucleic acid fractions using Thermus thermophilus argonaute with applications in cancer diagnostics.
Song J, Hegge JW, Mauk MG, Chen J, Till JE, Bhagwat N, Azink LT, Peng J, Sen M, Mays J, Carpenter EL, van der Oost J, Bau HH. Nucleic acids research. 2020 Feb 28;48(4):e19

Clinical Utility of Plasma Cell-Free DNA in Adult Patients with Newly Diagnosed Glioblastoma: A Pilot Prospective Study.
Bagley SJ, Nabavizadeh SA, Mays JJ, Till JE, Ware JB, Levy S, Sarchiapone W, Hussain J, Prior T, Guiry S, Christensen T, Yee SS, Nasrallah MP, Morrissette JJD, Binder ZA, O'Rourke DM, Cucchiara AJ, Brem S, Desai AS, Carpenter EL. Clinical cancer research : an official journal of the American Association for Cancer Research. 2020 Jan 15;26(2):397-407 Epub 2019 Oct 30

Imaging and histopathologic correlates of plasma cell-free DNA concentration and circulating tumor DNA in adult patients with newly diagnosed glioblastoma.
Nabavizadeh SA, Ware JB, Guiry S, Nasrallah MP, Mays JJ, Till JE, Hussain J, Abdalla A, Yee SS, Binder ZA, O'Rourke DM, Brem S, Desai AS, Wolf R, Carpenter EL, Bagley SJ. Neuro-oncology advances. 2020 Jan-Dec;2(1):vdaa016 Epub 2020 Feb 27

Correction: Flow based single cell analysis of the immune landscape distinguishes Barrett's esophagus from adjacent normal tissue.
Sen M, Hahn F, Black TA, DeMarshall M, Porter W, Snowden E, Yee SS, Tong F, Ferguson M, Fleshman EN, Nakagawa H, Falk GW, Ginsberg GG, Kochman ML, Blaesius R, Rustgi AK, Carpenter EL. Oncotarget. 2019 Aug 20;10(49):5119

Flow based single cell analysis of the immune landscape distinguishes Barrett's esophagus from adjacent normal tissue.
Sen M, Hahn F, Black TA, DeMarshall M, Porter W, Snowden E, Yee SS, Tong F, Ferguson M, Fleshman EN, Nakagawa H, Falk GW, Ginsberg GG, Kochman ML, Blaesius R, Rustgi AK, Carpenter EL. Oncotarget. 2019 Jun 4;10(38):3592-3604

Hepatocytes direct the formation of a pro-metastatic niche in the liver.
Lee JW, Stone ML, Porrett PM, Thomas SK, Komar CA, Li JH, Delman D, Graham K, Gladney WL, Hua X, Black TA, Chien AL, Majmundar KS, Thompson JC, Yee SS, O'Hara MH, Aggarwal C, Xin D, Shaked A, Gao M, Liu D, Borad MJ, Ramanathan RK, Carpenter EL, Ji A, de Beer MC, de Beer FC, Webb NR, Beatty GL. Nature. 2019 Mar;567(7747):249-252 Epub 2019 Mar 6

Clinical Implications of Plasma-Based Genotyping With the Delivery of Personalized Therapy in Metastatic Non-Small Cell Lung Cancer.
Aggarwal C, Thompson JC, Black TA, Katz SI, Fan R, Yee SS, Chien AL, Evans TL, Bauml JM, Alley EW, Ciunci CA, Berman AT, Cohen RB, Lieberman DB, Majmundar KS, Savitch SL, Morrissette JJD, Hwang WT, Elenitoba-Johnson KSJ, Langer CJ, Carpenter EL. JAMA oncology. 2019 Feb 1;5(2):173-180

Measurement and immunophenotyping of pleural fluid EpCAM-positive cells and clusters for the management of non-small cell lung cancer patients.
Thompson JC, Fan R, Black T, Yu GH, Savitch SL, Chien A, Yee SS, Sen M, Hwang WT, Katz SI, Feldman M, Vachani A, Carpenter EL. Lung cancer (Amsterdam, Netherlands). 2019 Jan;127:25-33 Epub 2018 Nov 19

Rare Event Phenotyping and Molecular Characterization: Circulating Tumor Cells.
Sen M, Wang L, Yu L, Carpenter EL. Methods in molecular biology (Clifton, N.J.). 2019;2032:213-226

An integrated enrichment system to facilitate isolation and molecular characterization of single cancer cells from whole blood.
Yu L, Sa S, Wang L, Dulmage K, Bhagwat N, Yee SS, Sen M, Pletcher CH Jr, Moore JS, Saksena S, Dixon EP, Carpenter EL. Cytometry. Part A : the journal of the International Society for Analytical Cytology. 2018 Dec;93(12):1226-1233

miRNA Profiling of Magnetic Nanopore-Isolated Extracellular Vesicles for the Diagnosis of Pancreatic Cancer.
Ko J, Bhagwat N, Black T, Yee SS, Na YJ, Fisher S, Kim J, Carpenter EL, Stanger BZ, Issadore D. Cancer research. 2018 Jul 1;78(13):3688-3697 Epub 2018 May 7

An integrated flow cytometry-based platform for isolation and molecular characterization of circulating tumor single cells and clusters.
Bhagwat N, Dulmage K, Pletcher CH Jr, Wang L, DeMuth W, Sen M, Balli D, Yee SS, Sa S, Tong F, Yu L, Moore JS, Stanger BZ, Dixon EP, Carpenter EL. Scientific reports. 2018 Mar 22;8(1):5035

Influence of TP53 Mutation on Survival in Patients With Advanced EGFR-Mutant Non-Small-Cell Lung Cancer.
Aggarwal C, Davis CW, Mick R, Thompson JC, Ahmed S, Jeffries S, Bagley S, Gabriel P, Evans TL, Bauml JM, Ciunci C, Alley E, Morrissette JJD, Cohen RB, Carpenter EL, Langer CJ. JCO precision oncology. 2018;2018 Epub 2018 Aug 31

Feasibility of monitoring advanced melanoma patients using cell-free DNA from plasma.
Gangadhar TC, Savitch SL, Yee SS, Xu W, Huang AC, Harmon S, Lieberman DB, Soucier D, Fan R, Black TA, Morrissette JJD, Salathia N, Waters J, Zhang S, Toung J, van Hummelen P, Fan JB, Xu X, Amaravadi RK, Schuchter LM, Karakousis GC, Hwang WT, Carpenter EL. Pigment cell & melanoma research. 2018 Jan;31(1):73-81 Epub 2017 Oct 23

Combining Machine Learning and Nanofluidic Technology To Diagnose Pancreatic Cancer Using Exosomes.
Ko J, Bhagwat N, Yee SS, Ortiz N, Sahmoud A, Black T, Aiello NM, McKenzie L, O'Hara M, Redlinger C, Romeo J, Carpenter EL, Stanger BZ, Issadore D. ACS nano. 2017 Nov 28;11(11):11182-11193 Epub 2017 Oct 17

A magnetic micropore chip for rapid (<1 hour) unbiased circulating tumor cell isolation and in situ RNA analysis.
Ko J, Bhagwat N, Yee SS, Black T, Redlinger C, Romeo J, O'Hara M, Raj A, Carpenter EL, Stanger BZ, Issadore D. Lab on a chip. 2017 Sep 12;17(18):3086-3096

Flow Cytometric Methods for Circulating Tumor Cell Isolation and Molecular Analysis.
Bhagwat N, Carpenter EL. Advances in experimental medicine and biology. 2017;994:105-118

Enumeration, Dielectrophoretic Capture, and Molecular Analysis of Circulating Tumor Cells.
Yee SS, Carpenter EL. Methods in molecular biology (Clifton, N.J.). 2017;1634:193-202

Detection of Therapeutically Targetable Driver and Resistance Mutations in Lung Cancer Patients by Next-Generation Sequencing of Cell-Free Circulating Tumor DNA.
Thompson JC, Yee SS, Troxel AB, Savitch SL, Fan R, Balli D, Lieberman DB, Morrissette JD, Evans TL, Bauml J, Aggarwal C, Kosteva JA, Alley E, Ciunci C, Cohen RB, Bagley S, Stonehouse-Lee S, Sherry VE, Gilbert E, Langer C, Vachani A, Carpenter EL. Clinical cancer research : an official journal of the American Association for Cancer Research. 2016 Dec 1;22(23):5772-5782 Epub 2016 Sep 6

A novel approach for next-generation sequencing of circulating tumor cells.
Yee SS, Lieberman DB, Blanchard T, Rader J, Zhao J, Troxel AB, DeSloover D, Fox AJ, Daber RD, Kakrecha B, Sukhadia S, Belka GK, DeMichele AM, Chodosh LA, Morrissette JJ, Carpenter EL. Molecular genetics & genomic medicine. 2016 Jul;4(4):395-406 Epub 2016 Feb 28

Circulating Tumor Cells, DNA, and mRNA: Potential for Clinical Utility in Patients With Melanoma.
Xu MJ, Dorsey JF, Amaravadi R, Karakousis G, Simone CB 2nd, Xu X, Xu W, Carpenter EL, Schuchter L, Kao GD. The oncologist. 2016 Jan;21(1):84-94 Epub 2015 Nov 27

Dielectrophoretic capture and genetic analysis of single neuroblastoma tumor cells.
Carpenter EL, Rader J, Ruden J, Rappaport EF, Hunter KN, Hallberg PL, Krytska K, O'Dwyer PJ, Mosse YP. Frontiers in oncology. 2014;4:201 Epub 2014 Jul 31

Dual CDK4/CDK6 inhibition induces cell-cycle arrest and senescence in neuroblastoma.
Rader J, Russell MR, Hart LS, Nakazawa MS, Belcastro LT, Martinez D, Li Y, Carpenter EL, Attiyeh EF, Diskin SJ, Kim S, Parasuraman S, Caponigro G, Schnepp RW, Wood AC, Pawel B, Cole KA, Maris JM. Clinical cancer research : an official journal of the American Association for Cancer Research. 2013 Nov 15;19(22):6173-82 Epub 2013 Sep 17

Antibody targeting of anaplastic lymphoma kinase induces cytotoxicity of human neuroblastoma.
Carpenter EL, Haglund EA, Mace EM, Deng D, Martinez D, Wood AC, Chow AK, Weiser DA, Belcastro LT, Winter C, Bresler SC, Vigny M, Mazot P, Asgharzadeh S, Seeger RC, Zhao H, Guo R, Christensen JG, Orange JS, Pawel BR, Lemmon MA, Mossé YP. Oncogene. 2012 Nov 15;31(46):4859-67 Epub 2012 Jan 23

Common variation at 6q16 within HACE1 and LIN28B influences susceptibility to neuroblastoma.
Diskin SJ, Capasso M, Schnepp RW, Cole KA, Attiyeh EF, Hou C, Diamond M, Carpenter EL, Winter C, Lee H, Jagannathan J, Latorre V, Iolascon A, Hakonarson H, Devoto M, Maris JM. Nature genetics. 2012 Oct;44(10):1126-30 Epub 2012 Sep 2

Targeting ALK in neuroblastoma--preclinical and clinical advancements.
Carpenter EL, Mossé YP. Nature reviews. Clinical oncology. 2012 May 15;9(7):391-9

Differential inhibitor sensitivity of anaplastic lymphoma kinase variants found in neuroblastoma.
Bresler SC, Wood AC, Haglund EA, Courtright J, Belcastro LT, Plegaria JS, Cole K, Toporovskaya Y, Zhao H, Carpenter EL, Christensen JG, Maris JM, Lemmon MA, Mossé YP. Science translational medicine. 2011 Nov 9;3(108):108ra114

Activation of human B cells by the agonist CD40 antibody CP-870,893 and augmentation with simultaneous toll-like receptor 9 stimulation.
Carpenter EL, Mick R, Rüter J, Vonderheide RH. Journal of translational medicine. 2009 Nov 11;7:93

Collapse of the CD27+ B-cell compartment associated with systemic plasmacytosis in patients with advanced melanoma and other cancers.
Carpenter EL, Mick R, Rech AJ, Beatty GL, Colligon TA, Rosenfeld MR, Kaplan DE, Chang KM, Domchek SM, Kanetsky PA, Fecher LA, Flaherty KT, Schuchter LM, Vonderheide RH. Clinical cancer research : an official journal of the American Association for Cancer Research. 2009 Jul 1;15(13):4277-87 Epub 2009 Jun 23

Functional analysis of CD8+ T cell responses to the onconeural self protein cdr2 in patients with paraneoplastic cerebellar degeneration.
Carpenter EL, Vance BA, Klein RS, Voloschin A, Dalmau J, Vonderheide RH. Journal of neuroimmunology. 2008 Jan;193(1-2):173-82 Epub 2007 Nov 28

Telomerase-specific T-cell immunity in breast cancer: effect of vaccination on tumor immunosurveillance.
Domchek SM, Recio A, Mick R, Clark CE, Carpenter EL, Fox KR, DeMichele A, Schuchter LM, Leibowitz MS, Wexler MH, Vance BA, Beatty GL, Veloso E, Feldman MD, Vonderheide RH. Cancer research. 2007 Nov 1;67(21):10546-55

Telomerase-based immunotherapy of cancer.
Carpenter EL, Vonderheide RH. Expert opinion on biological therapy. 2006 Oct;6(10):1031-9